Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: Implications for protein evolution in the RNA world
Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: Implications for protein evolution in the RNA world
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DOI：
10.1002/prot.10064
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发表时间：
2002-07-01
影响因子：
2.9
通讯作者：
Koonin, EV
中科院分区：
文献类型：
--
作者：
Aravind, L;Anantharaman, V;Koonin, EV
蛋白质序列和结构的比较表明，I类氨酰-tRNA合成酶的催化结构域，主要参与辅酶生物合成的核苷酸转移酶的相关家族，与UspA蛋白相关的核苷酸结合结构域，（USPA结构域）、光裂合酶、电子传递黄素蛋白和含PP环的ATP酶一起包含一类不同的α/β结构域，在HIGH-特征蛋白，UspA，和PP-ATPase。几条线的证据支持HUP域的单系性，排除其他三层的α/β折叠与通用的“罗斯曼样”拓扑结构。分支分析，与模式的结构和序列相似性作为离散字符，确定了三个主要的进化谱系内的HUP域类：PP-ATP酶;高超家族，其中包括I类阿尔斯和相关的核苷酸转移酶含有高签名在其核苷酸结合环;和以前未被识别的USPA样组，其中包括USPA域，电子传递黄素蛋白，和光解酶。对这三个主要谱系中不同家族的系统分布模式的研究表明，所有现代生命形式的最后共同祖先编码15-18种不同的α/β ATP酶和HUP类的核苷酸结合蛋白。这表明在最后一个普遍共同祖先（LUCA）之前HUP结构域的广泛辐射，在此期间，多个I类氨酰-tRNA合成酶仅在后期出现。因此，蛋白质结构域的实质性进化多样化发生在现代形式的蛋白质依赖性翻译机制建立之前，即，仍然存在于RNA世界中。(C)2002 Wiley-Liss，Inc.
Protein sequence and structure comparisons show that the catalytic domains of Class I aminoacyl-tRNA synthetases, a related family of nucleotidyltransferases involved primarily in coenzyme biosynthesis, nucleotide-binding domains related to the UspA protein (USPA domains), photolyases, electron transport flavoproteins, and PP-loop-containing ATPases together comprise a distinct class of alpha/beta domains designated the HUP domain after HIGH-signature proteins, UspA, and PP-ATPase. Several lines of evidence are presented to support the monophyly of the HUP domains, to the exclusion of other three-layered alpha/beta folds with the generic "Rossmann-like" topology. Cladistic analysis, with patterns of structural and sequence similarity used as discrete characters, identified three major evolutionary lineages within the HUP domain class: the PP-ATPases; the HIGH superfamily, which includes class I aaRS and related nucleotidyltransferases containing the HIGH signature in their nucleotide-binding loop; and a previously unrecognized USPA-like group, which includes USPA domains, electron transport flavoproteins, and photolyases. Examination of the patterns of phyletic distribution of distinct families within these three major lineages suggests that the Last Universal Common Ancestor of all modern life forms encoded 15-18 distinct alpha/beta ATPases and nucleotide-binding proteins of the HUP class. This points to an extensive radiation of HUP domains before the last universal common ancestor (LUCA), during which the multiple class I aminoacyl-tRNA synthetases emerged only at a late stage. Thus, substantial evolutionary diversification of protein domains occurred well before the modern version of the protein-dependent translation machinery was established, i.e., still in the RNA world. (C) 2002 Wiley-Liss, Inc.